I believe JJ Abrams left major clues in this movie as to the script for Star Trek (1)3. If you don't want spoilers, then stop reading right now.

Just like Into Darkness was a rethread of Wrath of Khan, the next movie will be a rethread of the Undiscovered Country where we will be on the brink/at war with the Klingons and the Enterprise will save thd day. Here is why
1) Admiral Marcus' statement that war is inevitable with the Klingons
2) Clear incursion by a Federation ship into not only Klingon Space but also their Homeworld Qu'onos.
3) Praxis, the moon of Qu'onos, is seen on screen and Kirk, Spock & Uhura land are arriving on Qu'onos. and it was clearly destroyed already (probably the reason for a portion of the planet being abandoned), something which occurred in the Unidiscovered Country in the Prime Timeline, decades after Into Darkness takes place. Praxis was destroyed as a result of over-mining brought forth by the Klingons heavy investments in their military, which was no doubt sped up by Nero's arrival into the past in the last movie and his wreaking havoc on the Klingon fleet, which likely forced even more ships to be built at a faster pace and thus accelerated the catastrophe. From the TNG episode where the Enterprise C is pulled into the future and doesn't complete its sacrifice mission to fight off a Romulan attack against a Klingon outpost, we know that this act was crucial in the Klingons' willingness to enter into an alliance with the Federation in the 24th century. Without it, the Klingons become even more aggressive and turn on the Federation, presumably in an attempt to survive and obtain more resources. Since Praxis' destruction is what triggers this need for military conquest, it is a safe bet that the early destruction of Praxis in JJ Abrams' timeline will bring fourth an early war with the Klingons.
4) Abrams' clear preference for action packed movies, which a Federation-Klingon war would no doubt provide.

So while I enjoyed Into Darkness, I was disappointed that JJ Abrams opted to rethread the past as opposed to come up with an original story line like in the first one. I thought the point of the reboot was to not be constrained by past events and just go to town. I did however like the fact that he injected moral dilemmas of present day into the story (use of extra judicial assassinations, response to attacks on civilians, etc) which was always what made Star Trek a good allegory. I strongly suspect they will remake the 3 most popular movies now, the first one having been Wrath of Khan, followed by Undiscovered country, and if I had to guess further, the fourth movie (which Chris Pine is already under contract for) would be a variation of The Voyage Home, assuming it is the last. Except instead of looking for humpback whales, they may end up preventing Romulus' star from going nova, and thus returning the original time line (or something very close to it)